About a year earlier while visiting his brother Hindal's camp in the desert, the 33-year-old Humayun's lecherous eyes fell upon Hamida Banu, the 13-year-old daughter of Mir Baba Dost, a religious guide to Hindal. Humayun wanted to sleep with the girl but the girl was unwilling and so was the father. The father was offered two lakhs of rupees and the girl was surrendered to Humayun. In September 1541, Hamida Banu gave birth to Akbar, while the couple honeymooned in the palace of Rana Prasad, the Hindu ruler of Amarkot. The same Akbar, born in a Hindu home, later blossomed into a Hindu-bating monster.
Humayun spent three years in the desert and was planning to return to Kandahar. His general Bairam Khan, who had remained in hiding in Gujarat after Humayun's defeat, came and joined the latter. On reaching Kandahar, Humayun was informed that his brothers Kamran and Askari were negotiating with Shah Hussain, ruler of Thatta to entrap Humayun and murder him. Scared at this news, Humayun left little Akbar with a lady in the harem in Kandahar and left for Persia. He was first well received on behalf of Shah Tahmasp of Persia by the governor of Seistan Later Humayun called upon the Shah. The Shah gave Humayun a force of 14,000 Muslim marauders on condition that Humayun was to cease to be a Sunni and become a follower of the Shia sect of Islam and cede Knadahar to the Persians after capture.

Equipped with this force, Humayun turned back. His immediate enemies were his own brothers of course! Kamran was the king of Kabul and Askari held Kandahar. Kamran had also seized Badakshan (south Bactria) from its governor Sulaiman Mirza, hired by Babur.

Humayun's forces captured the Garmsir region. He also captured Kandahar, gave it to the Persians. Askari fled from Humayun's camp but was later captured. and kept in close custody.

Humayun was now prevailed upon by his generals to invest Kandahar and retake it from the Persians. The Persians were surprised at the unexpected stab-in-the-back by a faithless Humayun. They were taken by surprise and did not offer any resistance and Kandahar was retaken by Humayun. Bairam who had been serving as a preceptor to the young Akbar, was put in charge of Kandahar.

Humayun now diverted his attention toward Kamran in Kabul. Kabul was besieged. Kamran's generals started defecting one by one to Humayun's side. Humayun promised to pardon Kamran if he made a personal submission. Not believing in his brother's Koranic oath, Kamran shut himself up inside the Kabul fort. As Humayun took possession of Kabul on November 15, 1545 A.D. Kamran fled to Ghazni. Humayun marched against Badakshan while Kamran swooped on Kabul and Ghazni and captured these towns. Kamran also got hold of the little Akbar. After capturing Badakshan, Humayun turned toward Kabul and thus was forced to reinstate the ruler of Badakshan. As Humayun's forces laid siege to Kabul, Kamran used to put the baby Akbar on the ramparts where the gunfire was the heaviest from Humayun's artillery. That stopped the gunfire for some time. Humayun continued to receive reinforcements while Kamran did not. In the end, Kamran sued for peace. But still unwilling to appear personally before Humayun, Kamran fled to Badakshan. He was captured and Humayun once again pardoned him and gave him the region of Kolab for Kamran's upkeep.